Run spectronaut, DIANN, FragPipe DIANN (SpecLib)
Send data through DEA with prolfqua
Label proteins by HUMAN, ECOLI, YEAST and look at various statistics
Number of DEA results when also Proteins with single peptide.
## [1] "SPECNAUT_default"
benchmark1$smc$summary
## # A tibble: 1 × 2
## nr_missing protein_Id
## <int> <int>
## 1 0 8714
benchmark1$plot_scatter()
benchmark1$plot_score_distribution()
## Picking joint bandwidth of 0.05
## Picking joint bandwidth of 0.05
## Picking joint bandwidth of 2.38
## Picking joint bandwidth of 0.0392
benchmark1$plot_ROC(xlim = 0.3)
## Warning: Removed 12492 rows containing missing values (`geom_path()`).
benchmark1$pAUC_summaries()
## $barp
##
## $ftable
## $ftable$content
## # A tibble: 6 × 5
## # Groups: contrast [2]
## contrast what AUC pAUC_10 pAUC_20
## <chr> <chr> <dbl> <dbl> <dbl>
## 1 B_vs_A diff 98.9 94.0 96.6
## 2 B_vs_A scaled.p.value 98.9 93.0 95.9
## 3 B_vs_A statistic 98.9 93.2 96.0
## 4 all diff 98.9 94.0 96.6
## 5 all scaled.p.value 98.9 93.0 95.9
## 6 all statistic 98.9 93.2 96.0
##
## $ftable$caption
## [1] "AUC, and pAUC at 0.1 and 0.2 FPR for (NC) protein level measurments, linear model"
##
## $ftable$digits
## [1] 2
benchmark1$plot_precision_recall(precision_lim = 0)
benchmark2$smc$summary
## # A tibble: 1 × 2
## nr_missing protein_Id
## <int> <int>
## 1 0 7613
benchmark2$plot_scatter()
benchmark2$plot_score_distribution()
## Picking joint bandwidth of 0.0464
## Picking joint bandwidth of 0.0464
## Picking joint bandwidth of 2.58
## Picking joint bandwidth of 0.0399
benchmark2$plot_ROC(xlim = 0.3)
## Warning: Removed 10971 rows containing missing values (`geom_path()`).
benchmark2$pAUC_summaries()
## $barp
##
## $ftable
## $ftable$content
## # A tibble: 6 × 5
## # Groups: contrast [2]
## contrast what AUC pAUC_10 pAUC_20
## <chr> <chr> <dbl> <dbl> <dbl>
## 1 B_vs_A diff 99.7 98.6 99.2
## 2 B_vs_A scaled.p.value 99.6 97.2 98.3
## 3 B_vs_A statistic 99.6 97.2 98.4
## 4 all diff 99.7 98.6 99.2
## 5 all scaled.p.value 99.6 97.2 98.3
## 6 all statistic 99.6 97.2 98.4
##
## $ftable$caption
## [1] "AUC, and pAUC at 0.1 and 0.2 FPR for (NC) protein level measurments, linear model"
##
## $ftable$digits
## [1] 2
benchmark2$plot_precision_recall(precision_lim = 0)
nr1 <- nr |> filter(nrPep == 1)
nr2 <- nr |> filter(nrPep == 2)
nr1 |> ggplot(aes(x = name, y = protein_Id)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
nr2 <- nr |> filter(nrPep == 2)
nr2 |> ggplot(aes(x = name, y = protein_Id)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
nr1 |> ggplot(aes(x = name, y = nrPeptides)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
nr2 |> ggplot(aes(x = name, y = nrPeptides)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
rocs <- bind_rows(lapply(all_RES, function(x){x$roc}))
rocs1 <- filter(rocs, nrPep == 1, what == "scaled.p.value", contrast == "B_vs_A")
rocs1 |> ggplot(aes(x = name, y = pAUC_10)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
rocs2 <- filter(rocs, nrPep == 2, what == "scaled.p.value", contrast == "B_vs_A")
rocs2 |> ggplot(aes(x = name, y = pAUC_10)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
rocs1 <- filter(rocs, nrPep == 1, what == "diff", contrast == "B_vs_A")
rocs1 |> ggplot(aes(x = name, y = pAUC_10)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
rocs2 <- filter(rocs, nrPep == 2, what == "diff", contrast == "B_vs_A")
rocs2 |> ggplot(aes(x = name, y = pAUC_10)) + geom_bar(stat="identity") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
## [1] "DIANN_314_relaxed" "DIANN_314" "DIANN_314_staggered_relaxed" "DIANN_314_staggered" "DIANN_FP_19_1"
## [6] "DIANN_FP_19_1_staggered" "DIANN_FP_312" "DIANN_FP_312_staggered" "SPECNAUT_default_Staggered" "SPECNAUT_default"
## [11] "SPECNAUT_NoImpute_Staggered"